RGE-GCN: Recursive Gene Elimination with Graph Convolutional Networks for RNA-seq based Early Cancer Detection

TL;DR

RGE-GCN is a novel framework combining graph convolutional networks and recursive gene elimination to identify predictive and interpretable biomarkers for early cancer detection from RNA-seq data.

Contribution

It introduces a unified pipeline that integrates feature selection and classification, improving biomarker discovery and classification accuracy over traditional methods.

Findings

Achieved higher accuracy and F1-scores than standard tools.

Selected genes aligned with known cancer pathways.

Demonstrated effectiveness across multiple cancer types.

Abstract

Early detection of cancer plays a key role in improving survival rates, but identifying reliable biomarkers from RNA-seq data is still a major challenge. The data are high-dimensional, and conventional statistical methods often fail to capture the complex relationships between genes. In this study, we introduce RGE-GCN (Recursive Gene Elimination with Graph Convolutional Networks), a framework that combines feature selection and classification in a single pipeline. Our approach builds a graph from gene expression profiles, uses a Graph Convolutional Network to classify cancer versus normal samples, and applies Integrated Gradients to highlight the most informative genes. By recursively removing less relevant genes, the model converges to a compact set of biomarkers that are both interpretable and predictive. We evaluated RGE-GCN on synthetic data as well as real-world RNA-seq cohorts of lung, kidney, and cervical cancers. Across all datasets, the method consistently achieved higher accuracy and F1-scores than standard tools such as DESeq2, edgeR, and limma-voom. Importantly, the selected genes aligned with well-known cancer pathways including PI3K-AKT, MAPK, SUMOylation, and immune regulation. These results suggest that RGE-GCN shows promise as a generalizable approach for RNA-seq based early cancer detection and biomarker discovery (https://rce-gcn.streamlit.app/ ).